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--- |
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license: bsd-3-clause |
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tags: |
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- spatial-data |
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- spatial-transcriptomics |
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- biology |
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- omics |
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- spatial-domains |
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--- |
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## Description |
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Full [`novae`](https://github.com/MICS-Lab/novae) dataset, including: |
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1. All the spatial transcriptomics samples used to train Novae |
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2. Protein samples used in the article |
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3. Some Visium and Visium HD samples |
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4. Synthetic data samples |
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You can download this dataset from the API, see [`novae.load_dataset`](https://mics-lab.github.io/novae/api/data/#novae.load_dataset) |
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See [here](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd) the list of available models trained on this dataset. |
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> [!NOTE] |
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> Note that Novae was trained on the **image-based** spatial transcriptomics samples. This means that it was **not** trained on the Visium/VisiumHD samples and the spatial proteomics samples. |
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## Cite us |
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Our article is published in [Nature Methods](https://www.nature.com/articles/s41592-025-02899-6). You can cite Novae as below: |
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```txt |
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Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data. |
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Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6 |
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``` |
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